3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera

The rapid and repeatable characterization of individual morphology has
advanced automated taxonomic classification. The most direct study of
evolutionary processes is, however, not from taxonomic description, but
rather of the evolution of the traits that comprise individuals and define
species. Repeatable signatures of individual morphology are crucial for
analyzing the response to selection at scale, and thus tracking
evolutionary trajectories through time and across species boundaries.
Here, we introduce our 3DKMI – an open-source MATLAB package designed for
the study of morphology using three-dimensional (3D) Krawtchouk moment
invariants. The volumetric features derived from the 3D images remain
stable under translation, scaling, and rotation and, for an image of size
128x128x128 can be computed in less than 0.1 seconds. We applied our
package as a case study on a collection of 300 X-ray computed tomography
scans of planktonic foraminifera specimens across five species to (1)
assess the invariance of the features under different transformations and
(2) analyze morphological differences among species based on the extracted
characteristics. We show that 3DKMI has the capacity to efficiently and
repeatedly characterize the signatures of individual morphology. In the
future, we hope that the 3D feature extraction technique 3DKMI will be
widely applied to digital collections to advance research in ecology and
evolution.